View Single Post
Old 06-23-2014, 08:18 AM   #20
Brian Bushnell
Super Moderator
 
Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707
Default

Quote:
Originally Posted by woodydon View Post
I can't find error-correcting option in bbmerge.sh. Also, in bbmap.sh, "out=" seems outputs reads instead of sam files. Could you please give me a hint? Thanks!
Woody,

bbmerge does not do error-correction; for that, you need to use the script "ecc.sh", e.g.

ecc.sh in=reads.fq out=corrected.fq

And as Genomax implied, all of my programs are sensitive to file name extensions. If you say "out=reads.fasta" you'll get fasta; if you say "out=reads.sam.gz", you'll get gzipped sam, and so forth.
Brian Bushnell is offline   Reply With Quote